How steady are you with a 4" disc grinder? Cut a piece of thin wall tube that slides over the spigot brg area of the input shaft to the correct length so that the unwanted piece [ 1/8"--3/16" ] of spigot shaft is exposed, Tape in place & using the tube end as a guide with a 1mm cutoff disc installed on your disc grinder slice off the unwanted portion, then very carefully bevel the first 1/16" @ 45° with a flap disc wheel on the same grinder.. job done ... half a banana
The 'plug' you see in the back of crank is actually the spigot bearing carrier, dont know about you guys in USA, but here in NZ the needle roller bearing & 'that' carrier are sold as one pre-assembled unit , ready to install.... make sure that your TKO is also not fouling on the spigot brg/needle roller on the shoulder where its dia increases to spline dia.
Have you run the motor with the TKO 600 in this condition where the input shaft interferes with crank, if so quite likely that the crank thrust bearing may have damage, center #3 main brg.